rs1509729

Variant names:

• chr11-109056756-C-T
• rs1509729

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.309 in 151,954 control chromosomes in the GnomAD database, including 7,400 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46955 AN: 151836 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 47010 AN: 151954 Hom.: 7400 Cov.: 32 AF XY: 0.313 AC XY: 23204 AN XY: 74234

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.310

Alfa AF: 0.296 Hom.: 9041

Bravo AF: 0.310

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1509729; hg19: chr11-108927483;